TC:E is a total conversion mod.
It means the physics, gameplay, story and a lot of points are different from the original.
You really need the etmain directory, not only because of the engine, but because a lot of ressources are taken from W:ET, like the player models (.mdm for example).
Try to remove the .pk3 from etmain and "enjoy"

No characters in console is one of the first things you'll notice.
And of course before to put a .pk3 "in production" on a server, admins/third-party creators test them on a test server.
The problem comes from servers which don't have the same .pk3 as them: theirs can replace the "default" ressources.
Once again it is a little detail, it can be fixed easily by doing
a special .pk3 in your tcetest directory and exiting the game before to join another server.
But in my oppinnion how i see it its just a big content pack. that make true combat series more independence than any other mod or even some commercial games out there. I realy want to see moddability in CQB but if it wont beat up the good ol true combat 1.2 i might ofcourse stick more to old.